Load and format input data

Input: Metadata bacteria: Database_MRB_isolates & database_raw, Mapping results: Mapping in 4 soils and feedback, Phylogeny: Tree compouted from 16s sequences

Phylogeny

Phylogeny without tree using radialNetwork()

Trees

Abundance of isolates in microbiome

Abundance of isolates from strain collection in microbiome datasets of the field & greenhouse Form quantitative values to quantitative. Abundant strains are defined as abundance > 0.1.

Amount of strains mapping to the abundant microbiome members at various locations.

Tree with mapping

The tree is annotated with the quantitative abundance data from mapping greenhouse root microbiome dataset and qualitative information on the abundance in field microbiome datasets in the field (Changins, Zurich, Ithaca) and in the greenhouse (Sheffield). The outermost ring indicates the strains used in growth assays. 

sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.3.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/Zurich
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] Cairo_1.6-0        networkD3_0.4      data.tree_1.0.0    ggnewscale_0.4.9  
##  [5] ggsci_3.0.0        wesanderson_0.3.6  ggtree_3.8.0       ape_5.7-1         
##  [9] reshape2_1.4.4     ggdendro_0.1.23    pheatmap_1.0.12    RColorBrewer_1.1-3
## [13] tibble_3.2.1       pander_0.6.5       ggpmisc_0.5.4-1    ggpp_0.5.4        
## [17] forcats_1.0.0      stringr_1.5.0      readr_2.1.4        tidyr_1.3.0       
## [21] readxl_1.4.2       ggplot2_3.4.3      magrittr_2.0.3     dplyr_1.1.2       
## [25] plyr_1.8.8        
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4       xfun_0.39          bslib_0.5.0        htmlwidgets_1.6.2 
##  [5] lattice_0.21-8     tzdb_0.4.0         yulab.utils_0.0.6  vctrs_0.6.3       
##  [9] tools_4.3.1        generics_0.1.3     parallel_4.3.1     fansi_1.0.4       
## [13] highr_0.10         pkgconfig_2.0.3    Matrix_1.5-4.1     ggplotify_0.1.0   
## [17] lifecycle_1.0.3    farver_2.1.1       compiler_4.3.1     treeio_1.24.1     
## [21] MatrixModels_0.5-1 munsell_0.5.0      SparseM_1.81       ggfun_0.1.0       
## [25] quantreg_5.95      htmltools_0.5.5    sass_0.4.6         lazyeval_0.2.2    
## [29] yaml_2.3.7         pillar_1.9.0       jquerylib_0.1.4    ellipsis_0.3.2    
## [33] MASS_7.3-60        cachem_1.0.8       nlme_3.1-162       tidyselect_1.2.0  
## [37] aplot_0.1.10       digest_0.6.31      stringi_1.7.12     purrr_1.0.1       
## [41] labeling_0.4.2     splines_4.3.1      fastmap_1.1.1      colorspace_2.1-0  
## [45] cli_3.6.1          patchwork_1.1.2    survival_3.5-5     utf8_1.2.3        
## [49] withr_2.5.0        scales_1.2.1       rmarkdown_2.22     igraph_1.5.0      
## [53] cellranger_1.1.0   hms_1.1.3          evaluate_0.21      knitr_1.43        
## [57] gridGraphics_0.5-1 rlang_1.1.1        Rcpp_1.0.11        tidytree_0.4.2    
## [61] glue_1.6.2         polynom_1.4-1      rstudioapi_0.14    jsonlite_1.8.5    
## [65] R6_2.5.1